New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	3512437 =	0 (0.000)	23 (1.190)	18/170	0.1	100%	intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
	?	NZ_CP009273	= 3646590	NA (NA)					pseudogene (3/379 nt)	BW25113_RS18165	hypothetical protein

AACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACA  >  NZ_CP009273/3646527‑3646663                                                                |                                                                           aaCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATaa                                                 <  2:165406/90‑1 (MQ=255)      tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAac                                            <  2:157276/90‑1 (MQ=255)                cTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACCCCCTAcccc                                  <  2:256107/90‑1 (MQ=255)                cTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTAcccc                                  <  1:263867/90‑1 (MQ=255)                cTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTAcccc                                  <  2:246933/90‑1 (MQ=255)                 tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTTACATAAAGAACACCCTAcccc                                  >  1:120094/1‑90 (MQ=255)                     gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACCCCCTACCCCCAAAt                             <  1:414546/90‑1 (MQ=255)                               aTGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGa                   <  2:12474/90‑1 (MQ=255)                                  aTCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATgg                <  1:362054/90‑1 (MQ=255)                                      cATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACaa            >  1:357509/1‑90 (MQ=255)                                          tCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTCCCCCCAAATTATATAAAGATGGACAATATc        <  2:103870/90‑1 (MQ=255)                                             gggACTTGTTGGCACCTTCCTTGGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTAGATAAAGATGGACAATATCTTg     >  2:397921/1‑90 (MQ=255)                                             gggACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTg     >  2:266019/1‑90 (MQ=255)                                                aCTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAaca                                           <  1:66682/49‑1 (MQ=255)                                                aCTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAaca                                           >  2:66682/1‑49 (MQ=255)                                                aCTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGaca  >  1:102827/1‑90 (MQ=255)                                                aCTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGaca  >  1:217338/1‑90 (MQ=255)                                                                |                                                                           AACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACA  >  NZ_CP009273/3646527‑3646663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.